Two trains in Barcelona's central Sants station were evacuated at around 8am on Wednesday, in order to allow police to search for an object shaped like a possible explosive device detected inside a suitcase.
The alarm was sounded by a security scanner in Sants, before Tedax, Spain's bomb disposal team, realised the case was travelling to the capital.
Shortly after Sants reopened, Madrid's Atocha station - the site of a bombing that killed 193 people 14 years ago - was shutdown on an order by police.
According to Cadena Ser, the bomb scares were triggered by a grenade-shaped belt buckle stored in the suitcase of a woman who was travelling from Barcelona to Madrid.
After tests by a bomb disposal team, Catalan police said the suitcase represented no danger.
Atocha, however, was evacuated around 10am, with commuters saying they were forced to "run out into the street", before authorities confirmed the false alarm and reopened the station less than an hour later.
The station was the site of Spain's deadliest militant attack in March 2004. More than 2,000 people were injured on top of the 193 killed. Police say it was carried out by Islamist militants inspired by Al-Qaeda.
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